Human activity and natural climate trends constitute a major threat to coral reefs worldwide. Models predict a significant reduction in reef spatial extension together with a decline in biodiversity in the relatively near future. In this context, monitoring programs to detect changes in reef ecosystems are essential. In recent years, coral reef mapping using remote sensing data has benefited from instruments with better resolution and computational advances in storage and processing capabilities. However, the water column represents an additional complexity when extracting information from submerged substrates by remote sensing that demands a correction of its effect. In this article, the basic concepts of bottom substrate remote sensing and water column interference are presented. A compendium of methodologies developed to reduce water column effects in coral ecosystems studied by remote sensing that include their salient features, advantages and drawbacks is provided. Finally, algorithms to retrieve the bottom reflectance are applied to simulated data and actual remote sensing imagery and their performance is compared. The available methods are not able to completely eliminate the water column effect, but they can minimize its influence. Choosing the best method depends on the marine environment, available input data and desired outcome or scientific application.

Widespread in the coastal zones of (sub)tropical regions, mangroves are an essential habitat for many animal species and provide subsistence resources for many human coastal communities. Among remote sensing techniques, synthetic aperture radar is a particularly advantageous method to monitor mangroves: images are not dependent on cloud cover and can provide information from forest understory. This article mapped mangrove forests in the southern coast of São Paulo State (Brazil) using frequency-based contextual classification of incoherent attributes derived from a multi-polarized Phased Array L-Band Synthetic Aperture Radar (PALSAR) image. The use of 10 incoherent attributes and only 3 Synthetic Aperture Radar (SAR) vegetation indices as input for digital classification showed the best accuracies with kappa index values of 0.739 and 0.734, respectively. HH polarization and SAR vegetation indices were the attributes that contributed most to the mangrove mapping procedure. The use of L-Band SAR data was effective for mapping mangrove areas, and therefore it is recommended as a tool for coastal management.

Monitoring chlorophyll-a (chl-a) concentrations is important for the management of water quality, because it is a good indicator of the eutrophication level in an aquatic system. Thus, our main purpose was to develop an alternative technique to monitor chl-a in time and space through remote sensing techniques. However, one of the limitations of remote sensing is the resolution. To achieve a high temporal resolution and medium space resolution, we used the Moderate Resolution Imaging Spectroradiometer (MODIS) 500-m reflectance product, MOD09GA, and limnological parameters from the Itumbiara Reservoir. With these data, an empirical (O14a) and semi-empirical (O14b) algorithm were developed. Algorithms were cross-calibrated and validated using three datasets: one for each campaign and a third consisting of a combination of the two individual campaigns. Algorithm O14a produced the best validation with a root mean square error (RMSE) of 30.4%, whereas O14b produced an RMSE of 32.41% using the mixed dataset calibration. O14a was applied to MOD09GA to build a time series for the reservoir for the year of 2009. The time-series analysis revealed that there were occurrences of algal blooms in the summer that were likely related to the additional input of nutrients caused by rainfall runoff. During the winter, however, the few observed algal blooms events were related to periods of atmospheric meteorological variations that represented an enhanced external influence on the processes of mixing and stratification of the water column. Finally, the use of remote sensing techniques can be an important tool for policy makers, environmental managers and the scientific community with which to monitor water quality.

Comparisons between in situ measurements of surface chlorophyll-a concentration (CHL) and ocean color remote sensing estimates were conducted during an oceanographic cruise on the Brazilian Southeastern continental shelf and slope, Southwestern South Atlantic. In situ values were based on fluorometry, above-water radiometry and lidar fluorosensor. Three empirical algorithms were used to estimate CHL from radiometric measurements: Ocean Chlorophyll 3 bands (OC3M_RAD), Ocean Chlorophyll 4 bands (OC4v4_RAD), and Ocean Chlorophyll 2 bands (OC2v4_RAD). The satellite estimates of CHL were derived from data collected by the MODerate-resolution Imaging Spectroradiometer (MODIS) with a nominal 1.1 km resolution at nadir. Three algorithms were used to estimate chlorophyll concentrations from MODIS data: one empirical - OC3M_SAT, and two semi-analytical - Garver, Siegel, Maritorena version 01 (GSM01_SAT), and Carder_SAT. In the present work, MODIS, lidar and in situ above-water radiometry and fluorometry are briefly described and the estimated values of chlorophyll retrieved by these techniques are compared. The chlorophyll concentration in the study area was in the range 0.01 to 0.2 mg·m^-3. In general, the empirical algorithms applied to the in situ radiometric and satellite data showed a tendency to overestimate CHL with a mean difference between estimated and measured values of as much as 0.17 mg/m³ (OC2v4_RAD). The semi-analytical GSM01 algorithm applied to MODIS data performed better (rmse 0.28, rmse-L 0.08, mean diff. -0.01 mg/m³) than the Carder and the empirical OC3M algorithms (rmse 1.14 and 0.36, rmse-L 0.34 and 0.11, mean diff. 0.17 and 0.02 mg/m³, respectively). We find that rmsd values between MODIS relative to the in situ radiometric measurements are < 26%, i.e., there is a trend towards overestimation of R_RS by MODIS for the stations considered in this work. Other authors have already reported over and under estimation of MODIS remotely sensed reflectance due to several errors in the bio-optical algorithm performance, in the satellite sensor calibration, and in the atmospheric-correction algorithm.

Chlorophyll concentrations (Chl a) data obtained from the Sea Viewing Wide Field of View Sensor (SeaWIFS) ocean color monthly images, Sea Surface Temperature (SST) pathfinder data obtained from the Advanced Very High Resolution Radiometer (AVHRR) sensors, and lobster (Panulirus argus) captures at the Cuban shelf were examined in order to analyze their spatial and temporal variability. A cross-correlation analysis was made between the standardized anomalies of the environmental variables (Chl a and SST) and the standardized anomalies of lobster captures for each fishery zones for the period between 1997 and 2005. For the deep waters adjacent to the fishing zones it was not observed a clear Chl a seasonality and on average the lowest values occurred south of the Island. It is with the three years lag that Chl a had the greatest numbers of significant correlation coefficients for almost all fishing zones. However, the cross-correlation coefficients with SST showed higher values with 1,5 year lag at all zones. Since the two environmental variables obtained by satellite sensors (SST and Chl a) influence the lobsters mainly during the planktonic life cycle, the cross-correlation with lobster captures begin to show significant indexes with lags of 1.5 years or more.