Abstract Salmonid incubators are a common means of introducing fish into rivers to re-establish or redistribute populations. Whilst survival rates of ova to emerging fry approaching 100% are reported, survival of <10% is not uncommon. Poor survival and compromised fitness in later life can result from many different environmental influences or aspects of incubator design and implementation. This paper reviews the effects of incubation conditions upon salmonid embryo mortality, development and fitness; in particular, the effects of factors influenced by, or a product of, artificial incubator design and operational protocol. This provides the basis to mitigate adverse effects through site-specific incubator design and operational protocols. In an example from a UK spate river, high sediment load effects were alleviated through the use of a novel incubation media, Enkamat, and a scouring capability to remove settled sediments from the incubator. In field trials, incubator siting and maintenance were also found to be essential to achieve high survival rates on a spate river.