Dispersal of organisms can influence the relationship between beta-diversity and regional productivity in heterogeneous environments. However, many ecosystems are also linked by fluxes of stressors, with an unknown influence on this relationship. In this study, we assess the relationship between beta-diversity (measured as Bray-Curtis dissimilarity) and regional productivity (measured as biovolume) under various levels of a stressor flux in meta-ecosystems that were composed of two marine micro-algae communities. We created heterogeneity by exposing one of the two communities to a herbicide and manipulated regional diversity by applying a dispersal gradient, which decreased beta-diversity. We applied four stressor flux levels, which homogenized the herbicide concentration between the communities over time. The stressor flux changed the relationship between beta-diversity and regional productivity by changing the effect of dispersal on regional productivity. In absence of the stressor flux, the relationship between beta-diversity and regional productivity was mostly not significant, but positive at the end of the experiment. This positive relationship was generated by a negative effect of dispersal on regional productivity, probably because dispersal disrupted local dynamics by removing organisms from the most-productive unstressed community. In presence of the stressor flux, the relationship between beta-diversity and regional productivity was often negative as dispersal now increased regional productivity. Dispersal increased regional productivity by increasing the productivity of the stressed community. This positive effect was stronger in the presence than in the absence of the stressor flux because the stressor flux reduced the concentration of the herbicide in the stressed community, where it facilitated recovery. Our study shows that stressor fluxes can strongly interact with the effects of dispersal on productivity and thus influence diversity-productivity relationships.