Didymosphenia geminata is an alga of major concern in temperate regions due to ongoing spread and unprecedented bloom formation. The aim of this study was to identify physical and chemical habitat conditions which affect D. geminata at catchment to patch scales. To examine this, we conducted a field-based survey of 55 distinct waterways across the South Island of New Zealand. D. geminata was detected at 82 % of waterways, grew within the periphyton at 54 % and at 25 % occurred as blooms. We tested 137 variables at scales ranging from catchment to small patches. The primary predictors of D. geminata waterway presence were still waterbodies (positive effect P < 0.05) and nitrate + nitrite (negative effect P = 0.08). D. geminata biomass was best explained by increasing river stability (P < 0.01) and decreasing nitrate + nitrite concentrations (P < 0.01). A patch-scale subsidy–stress relationship was also apparent with water velocity (P < 0.05). Our large-scale survey showed D. geminata was influenced by varied conditions at multiple spatial scales, preferentially occurring and blooming within stable, lake or dam-fed oligotrophic habitats. This work supports the finding that D. geminata blooms in response to nutrient limitation; however, results here reinforce that accrual is constrained by physical processes at multiple scales.