Assessment of population biology at early establishment stages is a fundamental component of conservation monitoring programmes, such as for invasive signal crayfish Pacifastacus leniusculus. Population structure, body condition (including its relation to density-dependence), spatial patterns and habitat relationships were examined between September and October 1997 along the lower River Stort catchment (Thames River catchment, UK). A higher proportion of females was observed at intermediate sizes, whereas the largest individuals were males. Body condition was positively associated with total crayfish abundance in females but not males. Principal components analysis of the population data (by gender and size) across sampling sites revealed three distinct groups (large males, large females, small crayfish of mixed gender), with large males having significantly (analysis of covariance) lower body condition. Multiple regression of crayfish population and habitat data revealed: increasing abundance was associated with high total suspended solids (e.g. burrowing behaviour) in all size/gender groups except medium and large males; decreasing abundances of large males and females with increasing hydrodynamic efficiency (i.e. Froude number); and increasing abundance of large males and females with increasing substratum roughness. Signal crayfish population structure in the River Stort suggests an elevated potential for dispersal and reinforcement throughout the River Lee catchment. The observed spatial and habitat segregation of crayfish by gender and size appears to reflect a female reproductive strategy that avoids contact between progeny and big aggressive/cannibalistic males. Furthermore, intra-male competition is the likely reason for the lower body condition of big males, given the lack of a negative relationship between male body condition and crayfish abundance. The comparison with established populations elsewhere shows that a sex-ratio biased towards females could be a good descriptor to detect invading populations. Potential threats posed by signal crayfish for the conservation of River Stort catchment are predation, competition and habitat alteration.