Biofouling triggers a chain of events that are deleterious to engineered systems providing safe water to the population and industry. The frequent use of dissolved biocides to combat biofilm growth has its own drawbacks, including the formation of noxious substances (e.g., organochlorinated compounds) and the discharge of significant amounts of nonspent biocides in the aquatic environment. This paper proposes affordable and robust approaches for water pretreatment to reduce organic (bio) and inorganic fouling to be implemented in developing rural areas. The pretreatment follows a sequential step strategy that includes particulate matter removal through optimized coagulation, phosphorus removal by iron oxide sorption using recovered inexpensive waste materials and, finally, an innovative biocidal treatment with functionalized particles. The following main experimental results were obtained: (1) coagulation treatment with aluminum sulfate at 0.03 mg L-1 led to the elimination of particulate matter fouling, as confirmed by the improved performance of a downstream membrane separation system; (2) in the sorption step, iron-covered waste sand taken from filter backwash water allowed a reduction of microbial available phosphorous to levels where biofilm growth is highly limited; and (3) the novel bactericidal process, using inexpensive commercial alumina particles functionalized with benzalkonium chloride, was able to reduce to zero the microbial load of a contaminated water stream within 1 h of residence time, without leaching the biocide to the water. Implementation of this concept represents an affordable and environmentally sustainable treatment system because the basic materials used have low cost and are easily available.