Small-scale fisheries around the world are increasingly facing pressures from a range of environmental, economic, and social sources. In order to sustain the societal benefits of small-scale fisheries, it is imperative to understand how fishing communities adapt to disturbances. Fishermen often catch multiple different species as an adaptation technique because diversifying one’s harvest portfolio like this creates multiple sources of income in case one species becomes unavailable. Here, we apply fisheries connectivity network analysis to characterize the harvest portfolios and timing of landings of dozens of small-scale fisheries in the Baja California Peninsula, Mexico. We found that network metrics like modularity and density varied by region and through time. The Pacific coast of Baja California displayed increasingly modular fisheries connectivity networks over the study period. This indicates that fisheries landings became less covaried with one another, implying an increased capacity to adapt by targeting species that are uncorrelated with each other through time. The remaining three Regions showed the opposite trend, where the covariance between fisheries increase over time. Differences in regional catch compositions also reflected the diversity of species caught around the Baja California Peninsula. A network perspective of small-scale fisheries landings provides insight into the resilience of multi-species fishing communities.