A field experiment was conducted to investigate the effects of intermittent versus continuous irrigation, together with different degrees of organic fertilization, on the growth and yield of hybrid rice, looking also at the functioning of the rhizosphere as this is a key element affecting crop performance. The crop management practices employed generally followed the recommendations of the System of Rice Intensification (SRI). The aim of the research was to learn how water management and organic fertilization together would affect crop outcomes. Under intermittent water application as recommended with SRI management (aerobic irrigation, AI), grain yield increased by 10.5–11.3%, compared to standard irrigation practice (continuous flooding, CF). The factor that contributed most to higher yield was increased number of grains per panicle. It was seen that under the range of organic fertilization treatments evaluated, intermittent irrigation compared with CF promoted greater dry matter production and higher leaf area index (LAI) during the main growth stages. Also, the combination of intermittent irrigation and organic material applications significantly increased soil redox potential (Eh), compared with CF, and also the numbers of actinomycetes in the rhizosphere soil. Actinomycetes were evaluated in this study as an indicator of aerobic soil biota. It was seen that with intermittent irrigation, the application of organic material improved the functioning of the rhizosphere and increased yield. However, these results based on 2 years of study reflect relatively short-term effects. The effects of longer-term water management and soil fertilization regimes should be also examined, to know whether these effects continue and, if they do, whether they become greater or less.