Small-scale, multispecific fisheries in the Gulf of California face significant challenges including limited species-specific catch data, uncertainty about climate change impacts, and insufficient biological information needed for traditional deterministic models. These knowledge gaps hamper efforts to forecast future conditions and develop appropriate management strategies accurately. The complexity of these multi-species fisheries, combined with data scarcity for many target species, creates substantial barriers to quantifying and addressing climate vulnerability. Deep learning approaches offer a promising alternative by leveraging available data to identify patterns and project trends despite these limitations, providing valuable insights for fisheries management in data-poor contexts. Here, we apply a Mixture of Expert, a deep learning forecasting models for small-scale, multi-specific fisheries in the Gulf of California under future climate change scenarios. Results show varied responses across marine habitats, with reef and benthic fish projected to experience substantial declines (-12.46% and -9.37%) during the 2050s-2060s, followed by recovery in the 2070s-2080s. Economic implications are significant, with reef fish facing projected losses of $1.2 million by the 2050s before recovering by the 2080s. Shapley Additive Explanations (SHAP) analysis was applied to evaluate the importance of features for each predictive model, the analysis revealed the effects of the temperature in different depths for each fishery, and the sensitive analysis pointed to the magnitude of the effect. Our findings suggest that climate impacts will not be uniform across the Gulf, necessitating region-specific management approaches and highlighting the value of maintaining diverse fishing portfolios to enhance resilience against climate-driven changes.