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Contemporary ecological landscape planning is often based on the assumption that small isolated habitat patches sustain relatively few species. Here, we suggest that for shallow lakes and ponds, the opposite can be true for some groups of organisms. Fish communities tend to be poor or even absent in small isolated lakes. However, submerged vegetation is often more abundant in such waterbodies. As a consequence of low fish biomass and high vegetation abundance, the richness of aquatic birds, plants, amphibians and invertebrates is often relatively high in small, shallow, isolated lakes. Although the rarity of fish is in line with expectations from the ruling paradigms about effects of habitat fragmentation in landscape ecology, the relative richness of various other groups of organisms in small ponds is opposite to these expectations. The case of shallow lakes illustrates that incorporating ecological interactions is essential to understanding the potential effects of habitat fragmentation. Single-species meta-population approaches may be misleading if ecological interactions are strong. A meta-community approach that explicitly incorporates biotic interactions, also those involving different trophic levels, is needed. Our diagnosis suggests that connection of isolated habitat fragments may in some cases reduce, rather than enhance, landscape-level biodiversity, and implies that biodiversity at the regional level will be maximized if the local habitat patches vary widely in size and degree of connectivity.