I did not find anything especially noteworthy in this choice. Yet there is a particular affinity between the sea and the whale: all regions lie under divine sovereignty. Jonah (peace be upon him) fled from dry land to the sea, only to be trapped there!
What is certain is that the fish that swallowed Jonah (peace be upon him) was an agent specially appointed by God. It deliberately crossed the path of the ship carrying him and carried out its mission with remarkable precision—from swallowing Jonah to casting him ashore. The choice of a fish as the means through which God’s miracle appeared is especially striking. That fish became Jonah’s mobile prison—and that very prison became his place of worship, his place of repentance and supplication, before finally guiding him to the shore of salvation.
Without doubt, this momentous event holds undiscovered mysteries that, God willing, will be unveiled by the Keeper of Secrets.
كَمَا حَكَى اللَّهُ حَتَّى انْتَهَى إِلَى سَاحِلِ الْبَحْرِ- فَإِذَا سَفِينَةٌ قَدْ شُحِنَتْ وَ أَرَادُوا أَنْ يَدْفَعُوهَا- فَسَأَلَهُمْ يُونُسُ أَنْ يَحْمِلُوهُ فَحَمَلُوهُ، فَلَمَّا تَوَسَّطُوا الْبَحْرَ بَعَثَ اللَّهُ حُوتاً عَظِيماً- فَحَبَسَ عَلَيْهِمُ السَّفِينَةَ مِنْ قُدَّامِهَا- فَنَظَرَ إِلَيْهِ يُونُسُ فَفَزِعَ مِنْهُ وَ صَارَ إِلَى مُؤَخَّرِ السَّفِينَةِ فَدَارَ إِلَيْهِ الْحُوتُ وَ فَتَحَ فَاهُ- فَخَرَجَ أَهْلُ السَّفِينَةِ فَقَالُوا فِينَا عَاصٍ فَتَسَاهَمُوا- فَخَرَجَ سَهْمُ يُونُسَ وَ هُوَ قَوْلُ اللَّهِ عَزَّ وَ جَلَّ «فَساهَمَ فَكانَ مِنَ الْمُدْحَضِينَ» فَأَخْرَجُوهُ فَأَلْقَوْهُ فِي الْبَحْرِ فَالْتَقَمَهُ الْحُوتُ وَ مَرَّ بِهِ فِي الْمَاءِ.
وَ قَدْ سَأَلَ بَعْضُ الْيَهُودِ أَمِيرَ الْمُؤْمِنِينَ ع عَنْ سِجْنٍ طَافَ أَقْطَارَ الْأَرْضِ بِصَاحِبِهِ، فَقَالَ يَا يَهُودِيُّ أَمَّا السِّجْنُ الَّذِي طَافَ أَقْطَارَ الْأَرْضِ بِصَاحِبِهِ- فَإِنَّهُ الْحُوتُ الَّذِي حُبِسَ يُونُسُ فِي بَطْنِهِ- فَدَخَلَ فِي بَحْرِ الْقُلْزُمِ ثُمَّ خَرَجَ إِلَى بَحْرِ مِصْرَ ثُمَّ دَخَلَ فِي بَحْرِ طَبَرِسْتَانَ ثُمَّ خَرَجَ فِي دِجْلَةَ الْغَوْرَاءِ ثُمَّ مَرَّتْ بِهِ تَحْتَ الْأَرْضِ حَتَّى لَحِقَتْ ...
Tafsir al-Qummi, vol. 1, p. 318
...As God has recounted, Jonah reached the shore. Suddenly, he saw a ship that had been loaded and was about to set sail. Jonah asked them to take him aboard as well. They agreed, and he boarded the ship. When they had reached the middle of the sea, God sent a huge fish and placed it in the ship’s path. When Jonah saw it, he was afraid and went to the stern; the fish followed him and opened its mouth. The people aboard rushed outside and said, “There is someone among us who has disobeyed.” They cast lots, and the lot fell to Jonah (as God says: “They cast lots, and he was among the losers”). They threw him into the sea, and the fish swallowed him and carried him through the waters.
One day, a Jewish man asked the Commander of the Faithful (peace be upon him), “I know of a prisoner who travelled around the world with his jailer.” The Imam replied, “O Jew, that prison was a fish that held Jonah in its belly. It emerged from the Sea of Qulzum, entered the Sea of Egypt, then the Sea of Tabaristan, passed through the Green Tigris, and continued beneath the earth until ...”