Carbon quantum dots are currently investigated to act as safe/potent alternatives for metal-based nanostructures to play the role of probes for environmental applications owing to their low toxicity, low cost, chemical inertness, biocompatibility and outstanding optical properties. The synthesis of biocide/fluorescent metal marker carbon quantum dots with hydrophilic character was performed via a quite simple and green technique. The natural biopolymer that was used in this study for the synthesis of carbon quantum dots is fragmented under strong alkaline conditions. Afterwards, under hydrothermal conditions, re-polymerization, aromatization and subsequent oxidation, the carbonic nanostructures were grown and clustered. Dialysis of the so-produced carbonic nanostructures was carried out to obtain highly purified/mono-dispersed carbon quantum dots with a size distribution of 1.5–6.5 nm. The fluorescence intensity of the synthesized carbon quantum dots under hydrothermal conditions for 3 h was affected by dialysis, however, the fluorescence intensity was significantly increased ca. 20 times. The synthesized carbon quantum dots were exploited as fluorescent markers in the detection of Zn²⁺ and Hg²⁺. The prepared carbon quantum dots also exhibited excellent antimicrobial potency against Bacillus cereus, Escherichia coli and Candida albicans. The detected minimal inhibitory concentration for the dialyzed CQDs towards the tested pathogens was 350–450 μL mL⁻¹. The presented approach is a simple and green technique for the scaled-up synthesis of biocide/fluorescent marker carbon quantum dots instead of metal-based nanostructures for environmental applications, without using toxic chemicals or organic solvents.