Egg pieces no longer count towards finishing a level, but instead add a random pet into the tank (always starting with three pets). Time Trial mode restricts the player to completing the first tank in five minutes and in ten minutes for the three subsequent tanks. Initially, up to 3 pets could be brought to the tank to help the player, though the player could buy the privilege to bring more pets each level later on with more shells. For the first time playing the game, at the end of each level of a tank, the player receives a new pet from the egg. Each level the player must earn enough money to buy 3 egg pieces to advance to the next level. Tanks 1-4 have five levels but Tank 5 has only one level in which a player must beat the final boss in order to complete the game. In adventure mode, a player advances through five tanks. Insaniquarium can be played in Adventure, Time Trial, Challenge Mode, or Virtual Tank.

The deluxe version of Insaniquarium contains eight different aliens, but in the original Java version there are four. The aliens must be clicked on repeatedly with the mouse pointer in order to defeat them. In addition to feeding fish, the player must protect the fish from aliens that periodically enter the tank and attempt to eat the fish. Each creature must be kept alive by feeding, whether through fish food bought by the player or other species of fish in the tank. Guppies and other fish drop money, which can be collected by the player and used to purchase fish food and upgrades, such as more aquatic creatures, more filling food, and powerful lasers to repel attackers. Players must manage a tank of guppies and other aquatic creatures, each stage begins with two guppies in the tank or one breeder which creates guppies. The following section was copied from Wikipedia. Shells are collected as the game progresses, and they can be used to create a custom Insaniquarium screen saver, to buy bonus pets or to increase the number of pets allowed in each tank. Insaniquarium Deluxe features enhanced graphics, new pets, new modes of gameplay, and a new type of currency called 'shells'.

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