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Mediterranean mountain ponds are excellent model systems for studying aquatic community changes and their underlaying mechanism. Their location within mountain landscapes results in isolated and poorly connected ponds. Furthermore, these dynamics ecosystems exhibit regional variation in environmental and spatial characteristics, making them ideal island ecosystems for metacommunities studies. This study investigates the influence of environmental and spatial factors on macroinvertebrate metacommunity structure in 23 isolated Mediterranean mountain ponds in Andalusia (south Spain). Macroinvertebrate combined pattern-based (Elements of Metacommunity Structure) and mechanistic (Redundancy Analysis and variation partitioning) approaches were employed to examine non-random distribution patterns in macroinvertebrates metacommunity structure. Additionally, by classifying macroinvertebrates into functional traits groups, allowed for an assessment of how different trait-based assemblages responded to these environmental and spatial drivers, providing a more nuanced understanding of community assembly. Results revealed a nested species distribution pattern, with species-poor ponds as subsets of richer ones. Redundancy Analysis identified hydroperiod and pond size as important environmental drivers, while fine-scale spatial variables had a greater influence than broad-scale ones. Although environmental factors explained more variation overall, no strong direct relationship with environmental variables was observed. The results suggests that nested patterns are driven by a combination of biogeographical processes, local environmental factors (pond size, hydroperiod), and fine-scale spatial structure. These findings emphasize the importance of considering habitat heterogeneity, connectivity, and regional species pools for effective conservation and management strategies of these pond ecosystems. Conservation efforts should prioritize maintaining connectivity between ponds and preserving those with high species richness to ensure the long-term persistence of macroinvertebrate metacommunities.