Fundamental differences in life history patterns of most indigenous freshwater stream species on oceanic islands and freshwater species in continental stream systems require important differences in design of appropriate aquatic survey methodologies. As an example of these issues, use of Instream Flow Incremental Methodology (IFIM) and the Index of Biotic Integrity (IBI) for describing island stream conditions are examined. Designed mainly for identifying optimal flow for salmonid fishes in the western United States, IFIM is difficult to apply to Hawaiian streams because of frequent flash floods in the Islands and because of the inherent difficulty of relating observed fish densities to total usable habitat in island streams. IBIs have been applied widely on the United States mainland as a technique for determining the health of a stream and aiding in stream fish conservation and management. Recently, there has been an attempt to establish an IBI for Hawaiian streams. Application of this technique to oceanic island streams raises a number of serious questions about the IBI’s validity for use in Hawaiian streams. Potential problems are inherent in the basic assumptions of the IBI. They result in unintended consequences when applied to oceanic island streams; examples include erroneously attributing naturally occurring differences in observed fish assemblages to human-induced environmental change, not accommodating differences in closed and open system dynamics linked to life cycles of indigenous stream species, and not understanding implications of low-diversity environments typical of remote oceanic islands. Past research on Hawaiian streams supports use of appropriate survey and analysis techniques such as those developed for the Pacific-Asia Biodiversity Transect (PABITRA) for use among islands of the tropical Pacific.