Piscivorous species like the Little Penguin (Eudyptula minor) are particularly at risk of being negatively impacted by pollution due to their heightened exposure through aquatic food chains. Therefore, determining the concentration of heavy metals in the fish prey of seabirds is an essential component of assessing such risk. In this study, we report on arsenic, cadmium, mercury, lead and selenium concentrations in three fish species, which are known to comprise a substantial part of the diet of Little Penguins at the urban colony of St Kilda, Melbourne, Australia. Metal concentrations in the fish sampled were generally within the expected limits, however, arsenic and mercury were higher than reported elsewhere. Anchovy (Engraulis australis) and sandy sprat (Hyperlophus vittatus) contained higher Hg concentrations than pilchard (Sardinops sagax), while sandy sprat and pilchard contained more selenium. We present these findings together with metal concentrations in Little Penguin blood and faeces, sampled within weeks of the fish collection. Mercury concentrations were highest in the blood, while faeces and fish prey species contained similar concentrations of arsenic and lead, suggesting faeces as a primary route of detoxification for these elements. We also investigated paired blood - faecal samples and found a correlation for selenium only. Preliminary data from stable isotope ratios in penguin blood indicate that changes in penguin blood mercury concentrations cannot be explained by trophic changes in their diet alone, suggesting a variation of bioavailable Hg within this semi-enclosed bay.