Otolith microchemistry can be used to determine the natal origins of fish. Solution-based inductively coupled plasma mass spectrometry (ICP-MS) analysis of water samples from tributary streams and beach locations around Lake Rotorua and Lake Rotoiti, Rotorua lakes district, New Zealand, indicate different and unique water isotopic chemistries at sample locations The concentrations of 24Mg, 43Ca, 55Mn, 85Rb, 88Sr and 137Ba differed significantly between tributary streams. The concentrations of 43Ca, 85Rb and 88Sr differed significantly between beaches. Discriminant function analysis (DFA) was used to classify the stream water samples from six tributary streams around Lake Rotorua and Lake Rotoiti with 100% accuracy. Beach water samples from seven sample locations around Lake Rotorua and Lake Rotoiti were classified with 64% accuracy. When grouped by lake, the water samples could be classified with 93% accuracy. The ambient water chemistry is a major influence on the otolith chemical composition. The water results indicate unique water chemistries and suggest using the microchemistry of otoliths to determine natal origins. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) was used for single spot analysis of otoliths of rainbow trout (Oncorhynchus mykiss) and common smelt (Retropinna retropinna) to determine concentrations of Mn, Zn, Rb, Sr and Ba. Juvenile trout otoliths from six spawning tributaries around Lake Rotorua and Lake Rotoiti could be classified to lake of origin with 98% accuracy overall. Using the DFA of 43 juvenile trout from spawning tributaries as the training set, classification coefficients were applied to analyses of elemental concentrations in the otolith nucleus of 92 adult wild rainbow of unknown natal origin captured in lakes Rotoiti and Rotorua and the Ohau Channel. Classification results suggest that the tributary streams of Lake Rotorua contribute the majority of individuals to the wild populations of adult rainbow trout of both lakes, comprising 88% of Lake Rotorua fish, 86% of Lake Rotoiti fish, and 100% of Ohau Channel fish. LA-ICP-MS spot analysis of common smelt otolith at the nuclei and edges provided information related to the movements between different chemical habitats across the fishes life. The concentrations of Mn, Zn, Rb, Sr and Ba differed significantly between the nucleus and edge spots in the smelt samples suggesting movement for some individuals. The scores from lake DFA classification functions showed two classes of smelt. Approximately 70% of smelt were lake residents and approximately 30% of smelt had migrated between the lakes. The nucleus results were compared with the known smelt capture location and the results are similar to the otolith analyses. The results of this investigation can be used to determine fish migration and assist with fisheries management decisions. Otolith microchemistry suggests that the construction of the wall diverting Lake Rotorua water into the Okere Arm of Lake Rotoiti is likely to impede migrations of wild rainbow trout from Lake Rotorua into Lake Rotoiti. Disruption of common smelt, migrations is likely to be less severe than for trout, but the prediction of smelt migration is less reliable because of the lower accuracy of classification.