This study investigates the best available methods for remote monitoring inland small-scale waterbodies, using remote sensing data from both Landsat-8 and Sentinel-2 satellites, utilizing a handheld hyperspectral device for ground truthing. Monitoring was conducted to evaluate water quality indicators: chlorophyll-a (Chl-a), colored dissolved organic matter (CDOM), and turbidity. Ground truthing was performed to select the most suitable atmospheric correction technique (ACT). Several ACT have been tested: dark spectrum fitting (DSF), dark object subtraction (DOS), atmospheric and topographic correction (ATCOR), and exponential extrapolation (EXP). Classical sampling was conducted first; then, the resulting concentrations were compared to those obtained using remote sensing analysis by the above-mentioned ACT. This research revealed that DOS and DSF achieved the best performance (an advantage ranging between 29% and 47%). Further, we demonstrated the appropriateness of the use of Sentinel-2 red and vegetation red edge reciprocal bands
1
/
B
4
×
B
6
for estimating Chl-a (
R
2
=
0.82
,
RMSE
=
14.52
mg
/
m
3
). As for Landsat-8, red to near-infrared ratio (
B
4
/
B
5
) produced the best performing model (
R
2
=
0.71
,
RMSE
=
39.88
mg
/
m
3
), but it did not perform as well as Sentinel-2. Regarding turbidity, the best model (
R
2
=
0.85
,
RMSE
=
0.87
NTU) obtained by Sentinel-2 utilized a single band (B4), while the best model (with
R
2
=
0.64
,
RMSE
=
0.90
NTU) using Landsat-8 was performed by applying two bands (
B
1
/
B
3
). Mapping the water quality parameters using the best performance biooptical model showed the significant effect of the adjacent land on the boundary pixels compared to pixels of deeper water.