There is a significant drive to identify a unified emission mechanism hidden behind carbon nanodots (CDs) to attain reliable control over their photoluminescence properties. This issue is addressed here by investigating the fluorescence response of citric acid and urea-based nitrogen doped carbon nanodots (NCDs) towards transition metal ions in solutions of different polarities/viscosities/hydrogen bonding strengths. The photoluminescence from NCDs upon excitation at 400 nm is quenched by metal ions such as chromium(VI), ruthenium(III) and iron(III) in two different polar solvents, protic water and aprotic dimethylsulphoxide (DMSO). This amplified luminescence quenching in polar solutions showed significant static quenching contributions. The quenching phenomenon highly depends on the excitation wavelength and solvent environment. The fluorescence quenching sequence reveals that pyridinic nitrogen-bases have a dominant influence on J-like emissive aggregates of NCDs. Similarly, oxygen-containing functional groups play a significant role in constructing H-aggregates of NCDs. The most intense emission is contributed by the J-like assembly of H-aggregates.