In the years 2007-2008 we assessed the ecological state in the Gidra river basin (the Malé Karpaty Mts). We assessed metrics on the basis of mayflies and stoneflies using software ASTERICS and compared them with those calculated from 1998–1999 data. The influence of selected environmental and microbiological factors was also evaluated. Two sample sites in the most natural tributary (the Kamenný potok) showed good ecological quality; in the middle reaches, site 3 (with the highest species diversity) scored very good ecological quality, whilst site 4 had average ecological quality. This does not represent a significant change compared to results from almost ten years before our research. Site 5 in the lower reach showed bad ecological quality and had declined by two classes compared to 1998–1999. We consider that the marked increase in microbial values has badly affected the ecological quality in the lower reaches.