Bacterial communities are shaped by diverse abiotic and biotic drivers. Species interactions and gene mobility both affect community response to perturbations. However, teasing apart the contribution of these factors is hard because it is difficult to modulate species interactions independently. Here we take advantage of temperature-dependent growth rates to explore how species competitiveness affects community dynamics and plasmid-borne resistance in the face of abiotic perturbations. We have built paired models and experimental systems to disentangle complex interactions in bacteria-plasmid communities and understand responses to environmental change. We developed a 3-bacteria, 2-plasmid system, where each plasmid can be hosted by two species and one species can host both plasmids, and an agent-based model of this system. We previously showed that species interactions could affect plasmid maintenance, even under conditions where plasmids were beneficial. Here we show that different incubation temperatures alter the relative competitiveness of the three bacteria, which changes the community response to environmental perturbations. Host and plasmid dynamics influence each other, with the permissive host allowing plasmid hitchhiking under conditions that select for the other plasmid. Together with an agent-based model, we show that relative competitiveness of the three species determines community stress response, with plasmid cost and host segregation rate shaping population dynamics. In addition, plasmid cost may be affected by stressors for which the plasmid does not carry known resistance genes (the orthogonal stress). Overall, we show the power of our combined approach, using experiments and models, to provide insight into complex bacterial community dynamics.