In the last decades, the presence of high As levels in groundwaters poses a serious limitation to the use of this resources for drinking purposes in several parts of the world. Treatment of As-rich waters selected iron oxides filters as more effective, low cost and selective technology. Green and biologically-driven pathways to synthetize new nanostructured iron oxy-hydroxides are becoming always more attractive. We tested the suitability of FeOOH nanoparticles (9–15 nm) produced by Klebsiella oxytoca strain DSM 29614 and encapsulated in EPS gel structure to treat arsenic rich water. Different gel:water volume ratios were tested to treat 5000 μg As/L solution. 20% FeEPS solution was able to remove 95% of As(V) while in 5% solution removal was reduced to 60%. Arsenic adsorption was very fast and follows pseudo-2nd order kinetic with maximum adsorption capacity reached at about 30 min. Adsorption followed Langmuir model for As(V) with qmax = 31.8 mgAs/gFe and BET for As(III) with 8 mgAs/gFe for the first layer in 10% FeEPS solution. FeEPS dried into powder showed noticeable removal only after 2 h, hence not suitable for drinking water treatment. Treatment of natural As levels in mimicked groundwaters showed 87–95% As(V) and 45–61% As(III) removal after 5 min. FeEPS gel immobilized onto bivalve shell debris was used in packed-bed filters. It retained 49.8 mgAs/gFe from 150 μg/L As(V) spiked groundwater before reaching breakthrough at 8000 BVs. Biologically produced FeEPS gel showed good potentialities as eco-friendly material to remove As from contaminated groundwater.