River floodplain systems are challenged by drought, which may trigger excess nutrient concentrations and greenhouse gas emissions. Increasingly frequent short-term droughts may exacerbate both problems by altering hydrological connectivity and thereby restructuring microbial communities and dissolved organic matter (DOM), which, in combination, may regulate sediment phosphorus and methane release. However, the combined effects of drought and connectivity on phosphorus and methane release via changes in DOM composition and microbial activity remain poorly understood. We incubated sediments from three floodplain sites along a hydrological connectivity gradient to the River Elbe and subjected them to two short-term drought intensities, corresponding to sediment moisture losses of 0.5–2.5% (moderate drought) and 19–21% (intense drought), followed by rewetting. Drought had surprisingly limited effects on phosphorus and methane release, while the site had a consistently higher impact and shaped the direction and magnitude of drought effects. Moreover, our results suggest that fluxes may be more pronounced at sites that were formerly well-connected to the river. Phosphorus was released under oxic conditions and was linked to heterotrophic microbial carbon use and humic-like DOM, implying that the effects of DOM-mediated microbial activity on phosphorus release need to be considered in future research efforts. Our findings suggest that long-term changes in hydrological connectivity, like lower discharge and changed DOM delivery, could have stronger effects on nutrient dynamics and microbial processes than short-term drought. Preserving floodplain connectivity is therefore critical to limiting nutrient and greenhouse gas release under climate change.