Characterizing temporary river ecosystem responses to flow regimes is vital for conserving their biodiversity and the services they provide to society. However, freshwater biomonitoring tools rarely reflect community responses to hydrological variations or flow cessation events, and those available have not been widely tested within temporary rivers. This study examines two invertebrate biomonitoring tools characterizing community responses to different flow-related properties: the “Drought Effect of Habitat Loss on Invertebrates” (DEHLI) and “Lotic-invertebrate Index for Flow Evaluation” (LIFE), which, respectively reflect community responses to habitat and hydraulic properties associated with changing flow conditions. Sub-seasonal (monthly) variations of LIFE and DEHLI were explored within two groundwater-fed intermittent rivers, one dries sporadically (a flashy, karstic hydrology—River Lathkill) and the other dries seasonally (a highly buffered flow regime—South Winterbourne). Biomonitoring tools were highly sensitive to channel drying and also responded to reduced discharges in permanently flowing reaches. Biomonitoring tools captured ecological recovery patterns in the Lathkill following a supra-seasonal drought. Some unexpected results were observed in the South Winterbourne where LIFE and DEHLI indicated relatively high-flow conditions despite low discharges occurring during some summer months. This probably reflected macrophyte encroachment, which benefitted certain invertebrates (e.g., marginal-dwelling taxa) and highlights the importance of considering instream habitat conditions when interpreting flow regime influences on biomonitoring tools. Although LIFE and DEHLI were positively correlated, the latter responded more clearly to drying events, highlighting that communities respond strongly to the disconnection of instream habitats as flows recede. The results highlighted short-term ecological responses to hydrological variations and the value in adopting sub-seasonal sampling strategies within temporary rivers. Findings from this study indicate the importance of establishing flow response guilds which group taxa that respond comparably to flow cessation events. Such information could be adopted within biomonitoring practices to better characterize temporary river ecosystem responses to hydrological variations.