We demonstrate the detection of magnetic particles carried by water in a continuous flow using an atomic magnetic gradiometer. Studies on three types of magnetic particles are presented: a single cobalt particle (diameter ~;150 mum, multi-domain), a suspension of superparamagnetic magnetite particles (diameter ~;1 mum), and ferromagnetic cobalt nanoparticles (diameter ~;10 nm, 120 kA/m magnetization). Estimated detection limits are 20 mum diameter for a single cobalt particle at a water flow rate 30 ml/min, 5x103 magnetite particles at 160 ml/min, and 50 pl for the specific ferromagnetic fluid at 130 ml/min. Possible applications of our method are discussed.