Spatially segregated ecosystems are frequently subsidized by cross-habitat linkages, but the extent to which the functional links between habitats influence local community attributes, such as consumer and food web structure is still poorly understood. Using the bidirectional linkage between benthic and pelagic habitats in floodplain lakes, we address this important question by looking for evidence of an optimal extent of habitat linkage supporting maximum taxonomic richness and mean trophic level. We then ask if there are significant changes in these local community attributes between historical and current communities, and if these reflect the history of species loss resulting from the intense human alteration of these lakes. We found a strong optimal response of maximum richness and mean trophic level along the pelagic-benthic gradient, both across and within individual lakes. This is consistent with the expectation of optimal resource availability along the habitat linkage gradient supporting more and taxonomically richer communities. Comparison between historical and current assemblages revealed a significant decrease in the optimal linkage for maximum richness in response to the history of species loss, but not for maximum mean trophic level, probably a response to the increased habitat homogenization and enhanced productivity caused by the recent history of nutrient-enrichment and habitat alteration. Our study provides strong evidence of high diversity and trophic level occurring at intermediate levels of coupling between pelagic and benthic resources, suggesting assemblage reliance on multiple production sources, and offers novel insight into the responses of this relationship to species loss due to human activities.