Yes there are some fundamental differences
Different types of water
the main challenge with aquariums compared with breeding terrestrial life, is that water differs a lot across the world, while the composition of air is virtually the same everywhere, whether over jungles, deserts, oceans or even cities.
Fish from the amazon rivers require slightly acidic water, with tannins but little minerals, while fish from the great african lakes need a higher pH and more dissolved minerals. Since saltwater is all about dissolved elements and its concentration is increased by evaporation, this becomes all the more critical with saltwater fish, which work to maintain their internal concentration of ions against that of the ocean around them.
Land animals drop their excrement on the ground, while fish swim in it, "breathe" the byproducts of bacterial breakdown of feces and suffer as the bacteria use up all the oxygen. Dealing with this while also maintaining "amazonian" or "tanganikan" water has kept many an aquarist busy. Land-animals are much simpler. The gecko dump its feces on the bottom of the cage and will happily breathe whatever air comes in your window.
On the microscopic scale, the difference between land and water is less pronounced. It is actually quite hard to breed in the lab many of the micro-organisms dwelling in soil. So much so that scientists has started sequencing DNA-fragments from soil to discover new species, never seeing them up front.