Small lentic habitats (ponds and wetlands) occur as discrete habitat patches across the landscape. We studied the colonization dynamics of small subalpine wetlands to understand how patterns of dispersal affect community composition and assembly. Experimental pools that varied in size and habitat complexity were placed 2 m from natural ponds of varying hydroperiods. We tested how species-level diversity in habitat patches varied as a function of 1) pool size, 2) pool habitat complexity, and 3) source-community characteristics. A total of 18 species and 8,527 aquatic animals colonized the 40 experimental pools after only nine days. Dipterans in the order Chironomidae contributed to 90% of all individuals and 30% of taxonomic richness. Two-way ANOVA revealed that species richness was greater in pools with higher habitat structure, but did not vary with pool size. Species richness also varied depending on the adjacent source of colonists; diversity was higher in pools next to vernal ponds than in those next to permanent ponds. This is consistent with the hypothesis that emigration rates from temporary habitats are higher than those from permanent. Our results suggest that conservation strategies for preserving biodiversity in small lentic habitats should focus on 1) maintaining mixtures of permanent and temporary habitats, and 2) on the habitat heterogeneity within habitats rather than the size of habitats. Understanding the biotic and abiotic variables that encourage colonization appears to be important for ensuring site-specific preservation of lentic invertebrate diversity.