Growth rates of shortfinned eels(Anguilla australis)from various locations in the Waikato basin, New Zealand, were determined by otolith examination. Two colour‐morphs from the Whangamarino Swamp exhibited different growth rates. Dark‐coloured eels (96% of the catch in low water levels) resided in the swamp; their growth was much slower than that of light‐coloured eels (40% of the catch in floods) which probably entered this habitat in flood waters from Lake Waikare, the Whangamarino River, or main wetland channels. Overall, growth rates were fastest in Lake Waikare followed by Lake Waahi, Lake Whangape, and Hakarimata pastoral streams. Dark‐coloured swamp eels were the slowest growing. Relative annual length increments ranged between 10 and 47 mm. Fast growth of eels in Lake Waikare may be the result of low densities owing to poor recruitment and heavy fishing pressure in recent years. Estimated age at threshold commercial size varied by 11 years throughout the Waikato.