Biological indicators based on fish assemblage characteristics are used to assess stream condition worldwide. Fish-based bioassessment poses challenges in Southern New England, the USA, due to the effects of within-watershed thermal gradients on fish assemblage types, low regional species richness, and lack of minimally disturbed sites. Dual multi-metric indices (MMI) of biological condition were developed for wadeable streams based on fish assemblage characteristics sampled across watershed landscapes with varying levels of human disturbance. A coldwater MMI was developed using streams with drainage area of <= 15 km(2), and a mixed-water MMI for streams with drainage areas of >15 km(2). For each MMI development, candidate metrics represented by ecological classes were sequentially tested by metric range, within-year precision, correlation with stream size, responsiveness to landscape-level human disturbances, and redundancy. Resultant coldwater and mixed-water MMI were composed of 5 and 7 metrics, respectively. Stream sites tended to score similarly when the two MMI were applied to transitional sites, i.e., drainage areas of 5-40 km(2). However, some sites received high scores from the mixed-water MMI and intermediate scores from the coldwater MMI. It was thus difficult to ascertain high-quality mixed-water streams from potential coldwater streams which currently support mixed-water assemblages due to ecological degradation. High-quality coldwater streams were restricted to stream sites with drainage areas <= 15 km(2). The newly developed fish-based MMI will serve as a useful management tool and the dual-MMI development approach may be applicable to other regions with thermal gradients that transition from coldwater to warmwater within watersheds. (C) 2009 Elsevier Ltd. All rights reserved.