Suspended sediment concentration (c) has been considered a critical environmental factor in reef habitats; however, the values and variations of c are not evident in a unique reef mainly created by crustose coralline algal concretions compared to abundant studies in coral reefs. The results of real-time and long-term monitoring of waves and c over the intertidal algal reef are reported because of the construction of an offshore industrial harbor near the reef. The real-time monitoring systems were based on techniques, including optical backscatter sensors (OBSs) for measuring c, pressure sensors for measuring waves, data loggers, and wireless networks for data transmission. The instruments sampled every hour and ran continuously and automatically for years. The OBS measurement was compared and validated with biweekly water sampling. A good correlation between the results of the two methods was observed. Nevertheless, more calibrations of OBSs in different seasons reduced the variance between the two methods over a year-long timescale. The year-long data showed a remarkable seasonal variation in c. The average c was approximately 140 mg/l during the winter season, while it was only approximately 70 mg/l during the summer season. The observed c was higher than that in other coral reef environments; the elevated and highly variable c, ranging from approximately 0 to 500 mg/l, may be one factor that creates the unique algae reef environment. The year-long measurement of waves and c showed that the variation in c was mainly due to the variation in waves in different seasons and was well correlated with the wave-induced bed shear stress. The real-time and long-term data measured by the system will aid in better understanding and providing useful environmental data for accessing future environmental changes and protecting reef habitats.