Settlement prediction based on monitoring data holds significant importance for engineering maintenance of seawalls. In practical engineering, the volume of the collected monitoring data is often limited due to the restrictions of devices and engineering budgets. Previous studies have applied the fractional-order grey model to time series prediction under the situation of limited data volume. However, the performance of the fractional-order grey model is easily affected by the inappropriate settings of fractional order. Also, the model cannot make dynamic predictions due to the characteristic of fixed step size. To solve the above problems, in this paper, the genetic algorithm with enhanced search capabilities was employed to solve the premature convergence problem. Additionally, to solve the problem of the fractional-order grey model associated with fixed step size, the real-time tracing algorithm was introduced to conduct equal-dimensionally recursive calculation. The proposed model was validated using monitoring data of four monitoring points at Haiyan seawall in Zhejiang province, China. The prediction performance of the proposed model was then compared with those of the fractional-order GM(1,1), integer-order GM(1,1), and fractal theory model. Results indicate that the proposed model significantly improves the prediction performance compared to other models.