Aquarium Fundamentals

Every animal in an aquarium lives in the same small volume of water. Food, salt, additives and new animals all come in. Waste, heat and the products of every living thing stay in, unless a water change, a skimmer, a filter or a person takes them out.

That's the single most important idea in aquarium keeping. In the ocean, nature keeps the water stable. In an aquarium, people do that job: by testing, changing water, maintaining equipment, feeding carefully and watching the animals.

It also means every mistake reaches every animal in that system at once. A wrong dose, a dead fish left to rot, or a failed pump affects the whole volume.

Things that build up: fish waste and leftover food break down into ammonia, then nitrate (Module 6), and release phosphate. Dissolved organics and settled waste (detritus) collect in the water, rock and sand.

Building up isn't automatically bad. Nitrate and phosphate are nutrients: at the right concentration they're food for algae, zooxanthellae and bacteria, and zero is harmful (Module 6). Ammonia is used as food too, at very low levels. Above the right level, each of them causes problems, and ammonia becomes toxic to fish. What matters is the concentration.

Things that get used up: animals that build shells and skeletons take calcium, alkalinity and magnesium out of the water every day. Trace elements are used too. Oxygen is used all the time and has to keep coming in from the surface.

The job is to keep each one at the right level, not to push it as high or as low as possible. The smaller the system, the faster these changes happen. A small tank can go from fine to dangerous much faster than a large one, which is why small systems need closer watching.

First, what live rock is

Live rock is rock taken from the ocean with its life still on it and inside it: bacteria, coralline algae, sponges, worms, tiny crustaceans and many other organisms living on its surface and in its pores. The rock itself isn't alive. It's called live because of everything living on and in it. Much of a system's biological filtration happens on and inside it (Module 8).

Dry rock is rock that starts out with nothing living on it. Over time in an aquarium it gains bacteria and some life, but nowhere near the variety of organisms that ocean live rock carries. Matured dry rock isn't the same thing as live rock, and shouldn't be treated as if it were.

A reef display holds corals, clams, invertebrates and fish, usually under strong lighting, and is often meant to be seen. A fish-only system holds fish and no corals or invertebrates. A fish and live rock system holds fish together with live rock, but no corals.

Quarantine and hospital systems keep new or sick animals apart from everything else (Module 23). Holding systems keep many animals in small tanks or containers for a short time, for example before sale or shipping. Breeding and grow-out systems hold breeding pairs, eggs, larvae and young fish.

Systems are also built in two common ways. In an all-in-one, the filter equipment sits in a chamber built into the back of the tank. In a sump system, water drains from the display to a separate tank underneath (the sump), where the equipment is, and a pump returns it. Both do the same jobs. Module 12 covers how they work and what goes wrong.

Cnidarians (corals, anemones, zoanthids, mushrooms, jellyfish) have stinging cells. Mollusks include clams, snails, limpets, chitons and nudibranchs. Crustaceans include shrimp and crabs, and they grow by shedding their shell (molting). Echinoderms include urchins, sea stars, brittle stars and sea cucumbers. Worms come in many forms: bristleworms and fireworms crawl through the rock, fan worms and Christmas tree worms live in tubes and filter the water with feathery crowns, and spaghetti worms stretch long thin tentacles across the sand. Sponges and tunicates (sea squirts) pump water through their bodies to feed. Many of these arrive on live rock.

Many of the most important organisms are hard to see: algae, from the pink coralline algae that coats rock to nuisance algae, tiny animals like copepods and amphipods (microfauna), and bacteria, which live on every surface and do much of the work of keeping the water clean (Module 8).

A healthy reef aquarium is a community. Removing or adding one part can change the others.

A scientific name has two parts: the genus (always written with a capital letter) and the species (always lower case), written in italics. Amphiprion ocellaris and Amphiprion percula are two different species of clownfish in the same genus. They look very alike, but they're different animals.

Living things are sorted into groups from broad to exact: kingdom, phylum, class, order, family, genus, species. In daily work you mostly need the last three. For example, clownfish belong to the damselfish family (Pomacentridae), and giant clams to the genus Tridacna, which includes Tridacna maxima, Tridacna crocea and Tridacna squamosa.

Use the scientific name whenever care, treatment or ordering depends on getting the animal exactly right. Two animals with similar common names can need very different care.

Look at the details: shape, color, pattern, size, number of tentacles or legs. Watch what it does: does it move, when is it out, what does it eat, where does it sit? Then compare with a trusted reference, not the first picture that looks a bit like it.

Some organisms look alike and act very differently. A harmless snail and a parasite can be the same size and color. A pest anemone can look like a coral. Some organisms sting or carry toxins (Module 2).

In photosynthesis, algae and the algae living inside corals and clams use light to turn carbon dioxide and water into sugar, giving off oxygen. It only happens while there's light.

In respiration, every living thing (fish, corals, clams, algae, bacteria) uses oxygen and gives off carbon dioxide, day and night.

So with the lights on, oxygen rises and CO2 falls, and pH goes up. With the lights off, only respiration is happening: oxygen falls, CO2 rises, and pH goes down (Module 6). A system is at its lowest oxygen near the end of the night, which is when a failed pump or air supply does the most damage.

In mutualism, both partners gain. A clownfish gets shelter in its anemone, and is protected from the stinging cells by a layer of mucus. The anemone gets food scraps, protection from fish that eat anemones, and nutrients from the clownfish's waste.

In commensalism, one partner gains and the other is neither helped nor harmed. In parasitism, one gains and the other is harmed. Small pyramidellid snails, for example, feed on giant clams and can kill them if they aren't found and removed (Module 28).

The most important partnership in a reef aquarium is the one inside corals, clams and many anemones: the algae called zooxanthellae.

The zooxanthellae photosynthesize and pass sugars to their host. In reef-building corals, as much as 90 percent of what the zooxanthellae make can go to the coral. In return, the host gives them a protected place to live, plus the carbon dioxide and nutrients they need. They're also responsible for much of a coral's color.

Giant clams carry their zooxanthellae in a system of tubes inside the body, and also feed by filtering particles from the water. Most hosts still need to feed as well as receive light.

When the host is stressed, it can lose its zooxanthellae and turn white. This is called bleaching. Bleaching is linked to stress such as unusual temperature or a sudden change in light. A bleached animal is starving, and if the zooxanthellae don't return, it can die.

Stony corals build their skeletons, giant clams and snails build their shells, and coralline algae builds a hard pink crust over rock and glass. Some tube worms, like Christmas tree worms, build hard tubes, and urchins have a hard shell-like skeleton.

To build, they take calcium and carbonate (measured as alkalinity) out of the water, along with magnesium. In a closed system, those levels fall every day unless something puts them back. That's what dosing, kalkwasser and calcium reactors are for (Module 19).

Because calcifiers use alkalinity, a system full of growing corals and clams needs its alkalinity checked more often than a fish-only system. When calcifiers stop growing, alkalinity use slows too, so a sudden change in use is itself a clue.

Animals with zooxanthellae get much of their energy from light, but most still eat. Filter feeders, like clams, many sponges and some corals, catch tiny particles and plankton from the water. Predators, like most fish and anemones, eat other animals or prepared foods. Grazers, like many snails and urchins, scrape algae off surfaces. Scavengers, like hermit crabs and bristleworms, eat leftovers.

Food that isn't eaten breaks down into ammonia, nitrate and phosphate (Module 6). At the right concentration those feed the system. Too much, and they cause problems. Feeding is always a balance: enough for the animals, not so much that the leftovers push the nutrients too high. Feeding is covered in depth in Module 26.

Some normal behavior looks alarming. Clownfish, and longfin clownfish in particular, often rest on the bottom and can look sick. A healthy one springs up and eats when food goes in. Some abnormal behavior is easy to miss: a carpet anemone shouldn't be deflating and reinflating often, or showing a gaping mouth.

Context matters too. Cloudy water, with an anemone deflated or clams looking off, while everything else in the system is fine, can be a spawning event rather than a disease.

Learn each animal's normal: how it sits, how it moves, how it eats, its color, when it's open or closed. Use the thinking loop from Module 1: observe first, check the facts, list the possible causes, and look at what changed. Write down what you see, even when it's normal. That record is what lets you see a change later.